I tried deleting preferences. Nothing.
The problem is in Logic 9. I can do 2 or 3 track just fine. It opens a floating score window, but when I do the fourth it opens below the arrange (not in a floating window as it should do), and some key commands just stops working.
Tested audio to score in Logic 8, and all is good there.
Looks like I have to do my audio to score in Logic 8 from now on.